February 16, 2021
I start the work with the data by finding the differentially expressed genes.
To do so, I perform the tests for comparison of the means of control and disease groups, starting with simple two sample for t-test. For each gene I also check the variances equality before comparing the groups’ means.
The number of differentiated genes proved to be really high, therefore I check whether the assumption on the normality of the distribution does not hinder the results by applying new test scheme:
I compare the result of taking the distribution into consideration with the previous assumption.
After getting gene differentiation, I proceed with enrichment analysis. I will start with ORA, then proceed into FCS methods.
## Title corrected_pvals ## 100 RNA transport 4.259285e-08 ## 133 Cell cycle 4.259285e-08 ## 305 MicroRNAs in cancer 1.182302e-07 ## 260 Alzheimer disease 1.960257e-06 ## 265 Prion disease 1.960257e-06 ## 295 Human T-cell leukemia virus 1 infection 1.960257e-06 ## 300 Pathways in cancer 2.529952e-06 ## 88 Metabolic pathways 4.283633e-06 ## 263 Huntington disease 4.283633e-06 ## 266 Pathways of neurodegeneration - multiple diseases 4.546480e-06 ## 115 Fanconi anemia pathway 6.612935e-06 ## 170 Focal adhesion 6.612935e-06 ## 304 Proteoglycans in cancer 6.612935e-06 ## 262 Amyotrophic lateral sclerosis 7.685330e-06 ## 101 mRNA surveillance pathway 2.554206e-05
## Title corrected_pvals ## 88 Metabolic pathways 2.368986e-08 ## 133 Cell cycle 2.368986e-08 ## 300 Pathways in cancer 2.368986e-08 ## 295 Human T-cell leukemia virus 1 infection 4.941884e-08 ## 170 Focal adhesion 1.231707e-07 ## 305 MicroRNAs in cancer 5.131701e-07 ## 159 Vascular smooth muscle contraction 5.800451e-07 ## 116 MAPK signaling pathway 2.139096e-06 ## 119 Rap1 signaling pathway 2.139096e-06 ## 125 Chemokine signaling pathway 4.895844e-06 ## 304 Proteoglycans in cancer 4.895844e-06 ## 148 PI3K-Akt signaling pathway 5.527751e-06 ## 144 Endocytosis 5.931361e-06 ## 177 Complement and coagulation cascades 5.931361e-06 ## 121 cGMP-PKG signaling pathway 7.034663e-06
## Title corrected_pvals ## 88 Metabolic pathways 9.001854e-28 ## 300 Pathways in cancer 1.231452e-22 ## 266 Pathways of neurodegeneration - multiple diseases 9.693740e-16 ## 295 Human T-cell leukemia virus 1 infection 1.234043e-15 ## 148 PI3K-Akt signaling pathway 2.047843e-14 ## 116 MAPK signaling pathway 6.369432e-14 ## 133 Cell cycle 6.369432e-14 ## 170 Focal adhesion 6.369432e-14 ## 260 Alzheimer disease 2.115722e-13 ## 305 MicroRNAs in cancer 3.002434e-13 ## 304 Proteoglycans in cancer 4.702153e-13 ## 265 Prion disease 3.590622e-12 ## 263 Huntington disease 4.907427e-12 ## 119 Rap1 signaling pathway 6.906820e-12 ## 294 Human papillomavirus infection 5.373930e-11
We can see the matlab output is definitely strange.
## P-value: 4.997284e-42
## Correlation coefficient: -0.6518573
## P-value: 0.261582
## Correlation coefficient: 0.06141717
## P-value: 2.1936e-26
## Correlation coefficient: -0.5360192
## P-value: 0.007659464
## Correlation coefficient: 0.1452507
## Title corrected_pvals ## 56 Glycerophospholipid metabolism 9.275123e-53 ## 171 ECM-receptor interaction 9.405913e-53 ## 238 Insulin resistance 1.147170e-52 ## 233 Relaxin signaling pathway 8.115912e-52 ## 240 AGE-RAGE signaling pathway in diabetic complications 9.085146e-52 ## 88 Metabolic pathways 5.763372e-51 ## 148 PI3K-Akt signaling pathway 6.818963e-51 ## 27 Arginine and proline metabolism 1.392011e-50 ## 254 Protein digestion and absorption 1.478016e-50 ## 305 MicroRNAs in cancer 1.478016e-50 ## 235 Parathyroid hormone synthesis, secretion and action 1.543308e-50 ## 173 Adherens junction 2.323504e-50 ## 273 Vibrio cholerae infection 2.323504e-50 ## 144 Endocytosis 3.092973e-50 ## 166 Apelin signaling pathway 3.250911e-50
## ORA CERNO Z_transform PLAGE ## enriched gene sets 114 200 263 338
## Number of joint enriched gene sets: 111
## Title pval_combined ## hsa04022 cGMP-PKG signaling pathway 0.000000e+00 ## hsa05206 MicroRNAs in cancer 0.000000e+00 ## hsa05200 Pathways in cancer 2.036205e-39 ## hsa01100 Metabolic pathways 6.959628e-39 ## hsa04110 Cell cycle 3.834775e-34 ## hsa04510 Focal adhesion 4.838081e-34 ## hsa05166 Human T-cell leukemia virus 1 infection 2.440812e-32 ## hsa05205 Proteoglycans in cancer 4.863737e-32 ## hsa05022 Pathways of neurodegeneration - multiple diseases 8.707401e-31 ## hsa04151 PI3K-Akt signaling pathway 8.386346e-30 ## hsa04010 MAPK signaling pathway 8.529154e-30 ## hsa05010 Alzheimer disease 1.119963e-29 ## hsa05020 Prion disease 3.556770e-29 ## hsa04360 Axon guidance 6.058880e-29 ## hsa04015 Rap1 signaling pathway 6.865159e-29